Host-specific generation and maintenance of Tomato bushy stunt virus defective interfering RNAs

Defective RNA Particles of Plant Viruses-Origin, Structure and Role in Pathogenesis

The genomes of RNA viruses may be monopartite or multipartite, and sub-genomic particles such as defective RNAs (D RNAs) or satellite RNAs (satRNAs) can be associated with some of them. D RNAs are small, deletion mutants of a virus that have lost essential functions for independent replication, encapsidation and/or movement. D RNAs are common elements associated with human and animal viruses, and they have been described for numerous plant viruses so far. Over 30 years of studies on D RNAs allow for some general conclusions to be drawn. First, the essential condition for D RNA formation is prolonged passaging of the virus at a high cellular multiplicity of infection (MOI) in one host. Second, recombination plays crucial roles in D RNA formation. Moreover, during virus propagation, D RNAs evolve, and the composition of the particle depends on, e.g., host plant, virus isolate or number of passages. Defective RNAs are often engaged in transient interactions with full-length viruses-they can modulate accumulation, infection dynamics and virulence, and are widely used, i.e., as a tool for research on cis-acting elements crucial for viral replication. Nevertheless, many questions regarding the generation and role of D RNAs in pathogenesis remain open. In this review, we summarise the knowledge about D RNAs of plant viruses obtained so far.

An in vitro reprogrammable antiviral RISC with size-preferential ribonuclease activity

Infection of Nicotiana benthamiana plants with Tomato bushy stunt virus (TBSV) mutants compromised for silencing suppression induces formation of an antiviral RISC (vRISC) that can be isolated using chromatography procedures. The isolated vRISC sequence-specifically degrades TBSV RNA in vitro, its activity can be down-regulated by removing siRNAs, and re-stimulated by exogenous supply of siRNAs. vRISC is most effective at hydrolyzing the ~4.8kb genomic RNA, but less so for a ~2.2kb TBSV subgenomic mRNA (sgRNA1), while the 3' co-terminal sgRNA2 of ~0.9kb appears insensitive to vRISC cleavage. Moreover, experiments with in vitro generated 5' co-terminal viral transcripts show that RNAs of ~2.7kb are efficiently cleaved while those of ~1.1kb or shorter are unaffected. The isolated antiviral ribonuclease complex fails to degrade ~0.4kb defective interfering RNAs (DIs) in vitro, agreeing with findings that in plants DIs are not targeted by silencing.

Replication of Plant Viruses

Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses co-infecting cells.

Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses coinfecting cells.

AGO/RISC-mediated antiviral RNA silencing in a plant in vitro system

AGO/RISC-mediated antiviral RNA silencing, an important component of the plant's immune response against RNA virus infections, was recapitulated in vitro. Cytoplasmic extracts of tobacco protoplasts were applied that supported Tombusvirus RNA replication, as well as the formation of RNA-induced silencing complexes (RISC) that could be functionally reconstituted with various plant ARGONAUTE (AGO) proteins. For example, when RISC containing AGO1, 2, 3 or 5 were programmed with exogenous siRNAs that specifically targeted the viral RNA, endonucleolytic cleavages occurred and viral replication was inhibited. Antiviral RNA silencing was disabled by the viral silencing suppressor p19 when this was present early during RISC formation. Notably, with replicating viral RNA, only (+)RNA molecules were accessible to RISC, whereas (-)RNA replication intermediates were not. The vulnerability of viral RNAs to RISC activity also depended on the RNA structure of the target sequence. This was most evident when we characterized viral siRNAs (vsiRNAs) that were particularly effective in silencing with AGO1- or AGO2/RISC. These vsiRNAs targeted similar sites, suggesting that accessible parts of the viral (+)RNA may be collectively attacked by different AGO/RISC. The in vitro system was, hence, established as a valuable tool to define and characterize individual molecular determinants of antiviral RNA silencing.

Host impact on the stability of a plant virus gene vector as measured by a new fluorescent local lesion passaging assay

Viruses can be used as vectors for transient expression of proteins in plants but frequently foreign gene inserts are not maintained stably over time due to recombination events. In this study the hypothesis was that the choice of plant host affects the foreign gene retention level by a Tomato bushy stunt virus (TBSV) vector expressing green fluorescent protein (GFP). To accomplish this, a novel virus vector integrity bioassay was developed based on an old concept, whereby RNA transcripts of the TBSV-GFP vector were rub-inoculated onto leaves of test plants, and at 3 days post inoculation (dpi), these leaves were used as inoculum for passage to cowpea (Vigna unguiculata), a local lesion host. Chlorotic lesions at points of virus infection were counted on cowpea at 4dpi and then the leaves were exposed to ultraviolet light to count green fluorescent foci. These tests with seven different plant species covering five families showed that the percentage of green fluorescent lesions varied on the cowpea indicator plants in a host-dependent manner. For instance, the vector was relatively unstable in Nicotiana benthamiana, tomato, bean, and spinach, but compared to those its stability in lettuce was significantly improved (~3-fold). This host-dependent effect suggests that some plants may present a more suitable environment than others to support or maintain optimum levels of virus vector-mediated foreign gene expression.

A viral satellite RNA induces yellow symptoms on tobacco by targeting a gene involved in chlorophyll biosynthesis using the RNA silencing machinery

Symptoms on virus-infected plants are often very specific to the given virus. The molecular mechanisms involved in viral symptom induction have been extensively studied, but are still poorly understood. Cucumber mosaic virus (CMV) Y satellite RNA (Y-sat) is a non-coding subviral RNA and modifies the typical symptom induced by CMV in specific hosts; Y-sat causes a bright yellow mosaic on its natural host Nicotiana tabacum. The Y-sat-induced yellow mosaic failed to develop in the infected Arabidopsis and tomato plants suggesting a very specific interaction between Y-sat and its host. In this study, we revealed that Y-sat produces specific short interfering RNAs (siRNAs), which interfere with a host gene, thus inducing the specific symptom. We found that the mRNA of tobacco magnesium protoporphyrin chelatase subunit I (ChlI, the key gene involved in chlorophyll synthesis) had a 22-nt sequence that was complementary to the Y-sat sequence, including four G-U pairs, and that the Y-sat-derived siRNAs in the virus-infected plant downregulate the mRNA of ChlI by targeting the complementary sequence. ChlI mRNA was also downregulated in the transgenic lines that express Y-sat inverted repeats. Strikingly, modifying the Y-sat sequence in order to restore the 22-nt complementarity to Arabidopsis and tomato ChlI mRNA resulted in yellowing symptoms in Y-sat-infected Arabidopsis and tomato, respectively. In 5'-RACE experiments, the ChlI transcript was cleaved at the expected middle position of the 22-nt complementary sequence. In GFP sensor experiments using agroinfiltration, we further demonstrated that Y-sat specifically targeted the sensor mRNA containing the 22-nt complementary sequence of ChlI. Our findings provide direct evidence that the identified siRNAs derived from viral satellite RNA directly modulate the viral disease symptom by RNA silencing-based regulation of a host gene.

Defective Interfering RNAs: Foes of Viruses and Friends of Virologists

Defective interfering (DI) RNAs are subviral RNAs produced during multiplication of RNA viruses by the error-prone viral replicase. DI-RNAs are parasitic RNAs that are derived from and associated with the parent virus, taking advantage of viral-coded protein factors for their multiplication. Recent advances in the field of DI RNA biology has led to a greater understanding about generation and evolution of DI-RNAs as well as the mechanism of symptom attenuation. Moreover, DI-RNAs are versatile tools in the hands of virologists and are used as less complex surrogate templates to understand the biology of their helper viruses. The ease of their genetic manipulation has resulted in rapid discoveries on cis-acting RNA replication elements required for replication and recombination. DI-RNAs have been further exploited to discover host factors that modulate Tomato bushy stunt virus replication, as well as viral RNA recombination. This review discusses the current models on generation and evolution of DI-RNAs, the roles of viral and host factors in DI-RNA replication, and the mechanisms of disease attenuation.

Tomato bushy stunt virus: a resilient model system to study virus-plant interactions

SUMMARY Taxonomy: Tomato bushy stunt virus (TBSV) (Fig. 1) is the type species of the plant-infecting Tombusvirus genus in the family Tombusviridae. Physical properties: TBSV virions are non-enveloped icosahedral T = 3 particles assembled from 180 coat protein subunits (42 kDa) whose arrangement causes a granular appearance on the surface structure. The particles are approximately 33 nm in diameter and composed of 17% ribonucleic acid and 83% protein. Encapsidated within the virion is the TBSV genome that consists of a positive-sense single-stranded RNA of approximately 4.8 kb, which lacks the 5'-cap or 3'-poly(A) tail typical for eukaryotic mRNAs.

HOST RANGE

In nature, TBSV has a fairly restricted host range, mostly encompassing a few dicotyledonous species in separate families, and affected agricultural crops comprise primarily vegetables. The experimental host range is broad, with over 120 plant species in more than 20 different families reported to be susceptible although in most plants the infection often remains localized around the site of entry. The differences between hosts with regards to requirements for cell-to-cell and long-distance movement have led to the development of TBSV as an attractive model system to obtain general insights into RNA transport through plants.

SYMPTOMS

SYMPTOMS induced by TBSV are largely dependent on the host genotype; they can vary from necrotic and chlorotic lesions, to a systemic mild or severe mosaic, or they may culminate in a lethal necrosis. The original TBSV isolates from tomato plants caused a mottle, crinkle and downward curling of leaves with the youngest leaves exhibiting tip necrosis upon systemic infection. Tomato fruit yield can be greatly reduced by virus infection. Plants may be stunted and a proliferation of lateral shoots leads to a bushy appearance of the infected tomato plants, hence the nomenclature of the pathogen. Useful sites: http://image.fs.uidaho.edu/vide/descr825.htm; http://www.ictvdb.rothamsted.ac.uk/ICTVdB/74010001.htm (general information); http://mmtsb.scripps.edu/viper/info_page.php?vipPDB=2tbv (structural information).

Integrity of nonviral fragments in recombinant Tomato bushy stunt virus and defective interfering RNA is influenced by silencing and the type of inserts

Recombinant plant viruses have the propensity to remove foreign inserts during replication. This process is virus-specific and occurs in a host-dependent manner. In the present study, we investigated the integrity of foreign inserts in recombinant plant viruses using a model system consisting of Tomato bushy stunt virus (TBSV) and its defective interfering RNA (DI). These were tested in Nicotiana benthamiana plants that were either wild type or transgenic for the green fluorescent protein (GFP) gene. GFP-derived inserts were retained in the recombinant TBSV and DI population that were inoculated onto GFP-transgenic N. benthamiana plants in which silencing of the GFP transgene was initiated, but they were removed from the virus and DIs that were maintained on wild-type plants. A foreign insert derived from an endogenous N. benthamiana gene encoding the H subunit of the magnesium chelatase (NbChlH) was deleted, whereas the fragment of an RNA-dependent RNA polymerase gene (NbRdRP1m) was retained in the recombinant TBSV population. These results demonstrate that the recombination of TBSV to remove nonviral fragments is influenced by silencing and the type of inserts.